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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.25.1

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/scrnaseq analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2025-01-21, 17:56 CET based on data in: /nfs/scratch/nf-core_work/nfs.data.COST_IBD.VASA-Seq.scrnaseq.run/23/a4bafb71d4ef631e58dcb845187bee


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        General Statistics

        Showing 0/130 rows and 6/12 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedDupsGCAvg lenMedian lenFailedSeqs
        24L007779_S1_L001
        9.5M
        3.8M
        40.3%
        3.0M
        31.9%
        0.8M
        24L007779_S1_L001_1
        2.7%
        45.0%
        151bp
        151bp
        27%
        9.5M
        24L007779_S1_L001_2
        30.9%
        49.0%
        151bp
        151bp
        27%
        9.5M
        24L007779_S1_L002
        9.7M
        3.9M
        40.3%
        3.1M
        31.9%
        0.8M
        24L007779_S1_L002_1
        2.9%
        44.0%
        151bp
        151bp
        18%
        9.7M
        24L007779_S1_L002_2
        30.2%
        49.0%
        151bp
        151bp
        27%
        9.7M
        24L007780_S2_L001
        8.7M
        4.0M
        46.3%
        3.3M
        37.9%
        0.7M
        24L007780_S2_L001_1
        3.8%
        39.0%
        151bp
        151bp
        27%
        8.7M
        24L007780_S2_L001_2
        30.9%
        45.0%
        151bp
        151bp
        27%
        8.7M
        24L007780_S2_L002
        8.9M
        4.1M
        46.1%
        3.4M
        37.8%
        0.7M
        24L007780_S2_L002_1
        4.0%
        39.0%
        150bp
        150bp
        18%
        8.9M
        24L007780_S2_L002_2
        30.4%
        45.0%
        151bp
        151bp
        27%
        8.9M
        24L007781_S3_L001
        8.6M
        3.8M
        44.4%
        3.1M
        36.5%
        0.7M
        24L007781_S3_L001_1
        3.6%
        42.0%
        151bp
        151bp
        27%
        8.6M
        24L007781_S3_L001_2
        26.7%
        47.0%
        151bp
        151bp
        27%
        8.6M
        24L007781_S3_L002
        8.7M
        3.9M
        44.3%
        3.2M
        36.4%
        0.7M
        24L007781_S3_L002_1
        3.6%
        42.0%
        151bp
        151bp
        18%
        8.7M
        24L007781_S3_L002_2
        26.1%
        47.0%
        151bp
        151bp
        27%
        8.7M
        24L007782_S4_L001
        11.4M
        5.3M
        46.7%
        4.4M
        38.8%
        0.9M
        24L007782_S4_L001_1
        3.4%
        41.0%
        151bp
        151bp
        27%
        11.4M
        24L007782_S4_L001_2
        36.7%
        47.0%
        151bp
        151bp
        36%
        11.4M
        24L007782_S4_L002
        11.6M
        5.4M
        46.7%
        4.5M
        38.8%
        0.9M
        24L007782_S4_L002_1
        3.4%
        41.0%
        151bp
        151bp
        18%
        11.6M
        24L007782_S4_L002_2
        35.9%
        47.0%
        151bp
        151bp
        36%
        11.6M
        24L007783_S5_L001
        6.4M
        2.8M
        43.3%
        2.3M
        35.6%
        0.5M
        24L007783_S5_L001_1
        3.7%
        39.0%
        151bp
        151bp
        27%
        6.4M
        24L007783_S5_L001_2
        32.8%
        45.0%
        151bp
        151bp
        27%
        6.4M
        24L007783_S5_L002
        6.5M
        2.8M
        43.2%
        2.3M
        35.6%
        0.5M
        24L007783_S5_L002_1
        3.7%
        39.0%
        151bp
        151bp
        18%
        6.5M
        24L007783_S5_L002_2
        32.0%
        45.0%
        151bp
        151bp
        27%
        6.5M
        24L007784_S6_L001
        7.2M
        5.1M
        71.2%
        4.6M
        63.8%
        0.5M
        24L007784_S6_L001_1
        3.7%
        35.0%
        151bp
        151bp
        18%
        7.2M
        24L007784_S6_L001_2
        29.7%
        45.0%
        151bp
        151bp
        18%
        7.2M
        24L007784_S6_L002
        7.3M
        5.2M
        71.2%
        4.7M
        63.8%
        0.5M
        24L007784_S6_L002_1
        3.9%
        35.0%
        151bp
        151bp
        9%
        7.3M
        24L007784_S6_L002_2
        29.1%
        45.0%
        151bp
        151bp
        18%
        7.3M
        2CLCmesc_0-0-3_S15
        22.6M
        8.8M
        39.1%
        7.7M
        34.1%
        1.1M
        2CLCmesc_0-0-3_S15_1
        8.4%
        42.0%
        100bp
        100bp
        36%
        22.6M
        2CLCmesc_0-0-3_S15_2
        32.6%
        54.0%
        201bp
        201bp
        36%
        22.6M
        2CLCmesc_0-0-4_S16
        17.2M
        8.6M
        49.8%
        7.4M
        43.1%
        1.2M
        2CLCmesc_0-0-4_S16_1
        2.8%
        41.0%
        100bp
        100bp
        18%
        17.2M
        2CLCmesc_0-0-4_S16_2
        34.7%
        53.0%
        201bp
        201bp
        36%
        17.2M
        2CLCmesc_003_RR_S3
        11.2M
        7.2M
        64.4%
        6.4M
        57.1%
        0.8M
        2CLCmesc_003_RR_S3_1
        3.1%
        43.0%
        100bp
        100bp
        18%
        11.2M
        2CLCmesc_003_RR_S3_2
        70.7%
        52.0%
        201bp
        201bp
        45%
        11.2M
        2CLCmesc_004_RR_S4
        11.9M
        8.7M
        73.0%
        7.6M
        64.1%
        1.1M
        2CLCmesc_004_RR_S4_1
        1.8%
        43.0%
        100bp
        100bp
        18%
        11.9M
        2CLCmesc_004_RR_S4_2
        72.4%
        52.0%
        201bp
        201bp
        45%
        11.9M
        2CLCmesc_011_RR_S18
        12.6M
        9.0M
        71.2%
        7.8M
        61.7%
        1.2M
        2CLCmesc_011_RR_S18_1
        1.9%
        41.0%
        100bp
        101bp
        18%
        12.6M
        2CLCmesc_011_RR_S18_2
        66.4%
        49.0%
        201bp
        201bp
        45%
        12.6M
        2CLCmesc_016_RR_S17
        9.9M
        6.0M
        60.5%
        5.2M
        52.1%
        0.8M
        2CLCmesc_016_RR_S17_1
        2.6%
        44.0%
        101bp
        101bp
        36%
        9.9M
        2CLCmesc_016_RR_S17_2
        60.1%
        53.0%
        201bp
        201bp
        45%
        9.9M
        2CLCmesc_1_RR_S9
        3.5M
        2.1M
        61.0%
        1.8M
        52.9%
        0.3M
        2CLCmesc_1_RR_S9_1
        2.1%
        43.0%
        100bp
        101bp
        18%
        3.5M
        2CLCmesc_1_RR_S9_2
        65.5%
        53.0%
        201bp
        201bp
        45%
        3.5M
        2CLCmesc_1_S1
        13.9M
        2.9M
        20.7%
        2.5M
        18.3%
        0.3M
        2CLCmesc_1_S1_1
        3.8%
        42.0%
        100bp
        100bp
        36%
        13.9M
        2CLCmesc_1_S1_2
        29.2%
        58.0%
        201bp
        201bp
        36%
        13.9M
        2CLCmesc_2_RR_S10
        8.3M
        4.8M
        57.2%
        4.1M
        49.0%
        0.7M
        2CLCmesc_2_RR_S10_1
        2.6%
        43.0%
        100bp
        101bp
        18%
        8.3M
        2CLCmesc_2_RR_S10_2
        67.6%
        53.0%
        201bp
        201bp
        45%
        8.3M
        2CLCmesc_2_S2
        11.3M
        1.8M
        16.1%
        1.5M
        13.6%
        0.3M
        2CLCmesc_2_S2_1
        3.4%
        43.0%
        100bp
        100bp
        36%
        11.3M
        2CLCmesc_2_S2_2
        26.4%
        59.0%
        201bp
        201bp
        36%
        11.3M
        2CLCmesc_3_RR_S11
        13.2M
        9.1M
        68.6%
        7.9M
        59.5%
        1.2M
        2CLCmesc_3_RR_S11_1
        3.5%
        42.0%
        100bp
        100bp
        18%
        13.2M
        2CLCmesc_3_RR_S11_2
        53.7%
        52.0%
        201bp
        201bp
        36%
        13.2M
        2CLCmesc_3_S5
        20.6M
        12.5M
        60.9%
        10.9M
        53.3%
        1.6M
        2CLCmesc_3_S5_1
        4.5%
        38.0%
        100bp
        100bp
        27%
        20.6M
        2CLCmesc_3_S5_2
        27.4%
        48.0%
        201bp
        201bp
        36%
        20.6M
        2CLCmesc_4_RR_S12
        12.0M
        5.6M
        46.5%
        4.8M
        40.1%
        0.8M
        2CLCmesc_4_RR_S12_1
        8.1%
        42.0%
        100bp
        100bp
        27%
        12.0M
        2CLCmesc_4_RR_S12_2
        35.3%
        56.0%
        201bp
        201bp
        45%
        12.0M
        2CLCmesc_4_S6
        15.9M
        9.4M
        59.1%
        8.1M
        51.0%
        1.3M
        2CLCmesc_4_S6_1
        9.5%
        36.0%
        100bp
        100bp
        27%
        15.9M
        2CLCmesc_4_S6_2
        34.2%
        46.0%
        201bp
        201bp
        45%
        15.9M
        2CLCmesc_5_RR_S13
        6.7M
        4.9M
        72.6%
        4.2M
        62.7%
        0.7M
        2CLCmesc_5_RR_S13_1
        4.1%
        38.0%
        100bp
        100bp
        18%
        6.7M
        2CLCmesc_5_RR_S13_2
        43.1%
        48.0%
        201bp
        201bp
        36%
        6.7M
        2CLCmesc_5_S7
        16.9M
        12.9M
        76.4%
        11.2M
        66.2%
        1.7M
        2CLCmesc_5_S7_1
        5.2%
        34.0%
        100bp
        100bp
        18%
        16.9M
        2CLCmesc_5_S7_2
        39.4%
        43.0%
        201bp
        201bp
        36%
        16.9M
        2CLCmesc_6_RR_S14
        5.4M
        1.9M
        34.9%
        1.5M
        28.5%
        0.3M
        2CLCmesc_6_RR_S14_1
        15.2%
        37.0%
        100bp
        100bp
        45%
        5.4M
        2CLCmesc_6_RR_S14_2
        36.0%
        49.0%
        201bp
        201bp
        45%
        5.4M
        2CLCmesc_6_S8
        9.3M
        3.8M
        40.8%
        3.2M
        34.1%
        0.6M
        2CLCmesc_6_S8_1
        16.2%
        35.0%
        100bp
        100bp
        45%
        9.3M
        2CLCmesc_6_S8_2
        33.7%
        48.0%
        201bp
        201bp
        45%
        9.3M
        combined_003
        33.8M
        16.0M
        47.5%
        14.1M
        41.7%
        1.9M
        combined_003_1
        8.4%
        42.0%
        100bp
        100bp
        36%
        22.6M
        combined_003_2
        32.6%
        54.0%
        201bp
        201bp
        36%
        22.6M
        combined_003_3
        3.1%
        43.0%
        100bp
        100bp
        18%
        11.2M
        combined_003_4
        70.7%
        52.0%
        201bp
        201bp
        45%
        11.2M
        combined_004
        29.0M
        17.2M
        59.3%
        15.0M
        51.7%
        2.2M
        combined_004_1
        2.8%
        41.0%
        100bp
        100bp
        18%
        17.2M
        combined_004_2
        34.7%
        53.0%
        201bp
        201bp
        36%
        17.2M
        combined_004_3
        1.8%
        43.0%
        100bp
        100bp
        18%
        11.9M
        combined_004_4
        72.4%
        52.0%
        201bp
        201bp
        45%
        11.9M
        combined_1
        17.3M
        5.0M
        28.7%
        4.4M
        25.2%
        0.6M
        combined_1_1
        3.8%
        42.0%
        100bp
        100bp
        36%
        13.9M
        combined_1_2
        29.2%
        58.0%
        201bp
        201bp
        36%
        13.9M
        combined_1_3
        2.1%
        43.0%
        100bp
        101bp
        18%
        3.5M
        combined_1_4
        65.5%
        53.0%
        201bp
        201bp
        45%
        3.5M
        combined_2
        19.6M
        6.6M
        33.6%
        5.6M
        28.6%
        1.0M
        combined_2_1
        3.4%
        43.0%
        100bp
        100bp
        36%
        11.3M
        combined_2_2
        26.4%
        59.0%
        201bp
        201bp
        36%
        11.3M
        combined_2_3
        2.6%
        43.0%
        100bp
        101bp
        18%
        8.3M
        combined_2_4
        67.6%
        53.0%
        201bp
        201bp
        45%
        8.3M
        combined_3
        33.8M
        21.6M
        63.9%
        18.8M
        55.7%
        2.8M
        combined_3_1
        4.5%
        38.0%
        100bp
        100bp
        27%
        20.6M
        combined_3_2
        27.4%
        48.0%
        201bp
        201bp
        36%
        20.6M
        combined_3_3
        3.5%
        42.0%
        100bp
        100bp
        18%
        13.2M
        combined_3_4
        53.7%
        52.0%
        201bp
        201bp
        36%
        13.2M
        combined_4
        27.9M
        15.0M
        53.7%
        12.9M
        46.3%
        2.1M
        combined_4_1
        9.5%
        36.0%
        100bp
        100bp
        27%
        15.9M
        combined_4_2
        34.2%
        46.0%
        201bp
        201bp
        45%
        15.9M
        combined_4_3
        8.1%
        42.0%
        100bp
        100bp
        27%
        12.0M
        combined_4_4
        35.3%
        56.0%
        201bp
        201bp
        45%
        12.0M
        combined_5
        23.6M
        17.8M
        75.3%
        15.4M
        65.2%
        2.4M
        combined_5_1
        5.2%
        34.0%
        100bp
        100bp
        18%
        16.9M
        combined_5_2
        39.4%
        43.0%
        201bp
        201bp
        36%
        16.9M
        combined_5_3
        4.1%
        38.0%
        100bp
        100bp
        18%
        6.7M
        combined_5_4
        43.1%
        48.0%
        201bp
        201bp
        36%
        6.7M
        combined_6
        14.7M
        5.7M
        38.6%
        4.7M
        32.1%
        1.0M
        combined_6_1
        16.2%
        35.0%
        100bp
        100bp
        45%
        9.3M
        combined_6_2
        33.7%
        48.0%
        201bp
        201bp
        45%
        9.3M
        combined_6_3
        15.2%
        37.0%
        100bp
        100bp
        45%
        5.4M
        combined_6_4
        36.0%
        49.0%
        201bp
        201bp
        45%
        5.4M

        STAR

        Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635

        Summary Statistics

        Summary statistics from the STAR alignment

        Showing 0/38 rows and 10/19 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedAvg. read lenAvg. mapped lenSplicesAnnotated splicesGT/AG splicesGC/AG splicesAT/AC splicesNon-canonical splicesMismatch rateDel rateDel lenIns rateIns len
        24L007779_S1_L001
        9.5M
        3.8M
        40.3%
        3.0M
        31.9%
        0.8M
        150.0bp
        141.2bp
        0.8M
        0.7M
        0.7M
        0.0M
        0.0M
        0.0M
        0.8%
        0.1%
        4.1bp
        0.0%
        1.6bp
        24L007779_S1_L002
        9.7M
        3.9M
        40.3%
        3.1M
        31.9%
        0.8M
        150.0bp
        141.2bp
        0.8M
        0.7M
        0.7M
        0.0M
        0.0M
        0.0M
        0.9%
        0.1%
        4.0bp
        0.0%
        1.6bp
        24L007780_S2_L001
        8.7M
        4.0M
        46.3%
        3.3M
        37.9%
        0.7M
        150.0bp
        141.4bp
        0.9M
        0.9M
        0.9M
        0.0M
        0.0M
        0.0M
        0.8%
        0.1%
        3.6bp
        0.0%
        1.4bp
        24L007780_S2_L002
        8.9M
        4.1M
        46.1%
        3.4M
        37.8%
        0.7M
        150.0bp
        141.5bp
        0.9M
        0.9M
        0.9M
        0.0M
        0.0M
        0.0M
        0.9%
        0.1%
        3.6bp
        0.0%
        1.4bp
        24L007781_S3_L001
        8.6M
        3.8M
        44.4%
        3.1M
        36.5%
        0.7M
        150.0bp
        142.1bp
        0.9M
        0.8M
        0.8M
        0.0M
        0.0M
        0.0M
        0.8%
        0.1%
        3.7bp
        0.0%
        1.4bp
        24L007781_S3_L002
        8.7M
        3.9M
        44.3%
        3.2M
        36.4%
        0.7M
        150.0bp
        142.1bp
        0.9M
        0.8M
        0.8M
        0.0M
        0.0M
        0.0M
        0.9%
        0.1%
        3.7bp
        0.0%
        1.4bp
        24L007782_S4_L001
        11.4M
        5.3M
        46.7%
        4.4M
        38.8%
        0.9M
        150.0bp
        140.2bp
        0.9M
        0.8M
        0.8M
        0.0M
        0.0M
        0.0M
        0.9%
        0.1%
        3.3bp
        0.0%
        1.5bp
        24L007782_S4_L002
        11.6M
        5.4M
        46.7%
        4.5M
        38.8%
        0.9M
        150.0bp
        140.2bp
        0.9M
        0.8M
        0.9M
        0.0M
        0.0M
        0.0M
        0.9%
        0.1%
        3.3bp
        0.0%
        1.5bp
        24L007783_S5_L001
        6.4M
        2.8M
        43.3%
        2.3M
        35.6%
        0.5M
        150.0bp
        140.4bp
        0.5M
        0.4M
        0.4M
        0.0M
        0.0M
        0.0M
        0.9%
        0.1%
        3.2bp
        0.0%
        1.4bp
        24L007783_S5_L002
        6.5M
        2.8M
        43.2%
        2.3M
        35.6%
        0.5M
        150.0bp
        140.4bp
        0.5M
        0.4M
        0.4M
        0.0M
        0.0M
        0.0M
        1.0%
        0.1%
        3.2bp
        0.0%
        1.4bp
        24L007784_S6_L001
        7.2M
        5.1M
        71.2%
        4.6M
        63.8%
        0.5M
        150.0bp
        143.5bp
        1.0M
        1.0M
        1.0M
        0.0M
        0.0M
        0.0M
        0.8%
        0.1%
        3.5bp
        0.1%
        1.5bp
        24L007784_S6_L002
        7.3M
        5.2M
        71.2%
        4.7M
        63.8%
        0.5M
        150.0bp
        143.5bp
        1.1M
        1.0M
        1.0M
        0.0M
        0.0M
        0.0M
        0.9%
        0.1%
        3.4bp
        0.1%
        1.5bp
        2CLCmesc_0-0-3_S15
        22.6M
        8.8M
        39.1%
        7.7M
        34.1%
        1.1M
        200.0bp
        183.3bp
        2.5M
        2.4M
        2.4M
        0.0M
        0.0M
        0.1M
        0.6%
        0.1%
        3.3bp
        0.0%
        1.5bp
        2CLCmesc_0-0-4_S16
        17.2M
        8.6M
        49.8%
        7.4M
        43.1%
        1.2M
        200.0bp
        185.4bp
        2.5M
        2.4M
        2.4M
        0.0M
        0.0M
        0.1M
        0.6%
        0.1%
        3.4bp
        0.1%
        1.8bp
        2CLCmesc_003_RR_S3
        11.2M
        7.2M
        64.4%
        6.4M
        57.1%
        0.8M
        200.0bp
        183.7bp
        0.5M
        0.4M
        0.4M
        0.0M
        0.0M
        0.1M
        0.8%
        0.1%
        3.5bp
        0.1%
        2.2bp
        2CLCmesc_004_RR_S4
        11.9M
        8.7M
        73.0%
        7.6M
        64.1%
        1.1M
        200.0bp
        186.2bp
        0.6M
        0.5M
        0.5M
        0.0M
        0.0M
        0.1M
        0.8%
        0.1%
        3.3bp
        0.1%
        2.2bp
        2CLCmesc_011_RR_S18
        12.6M
        9.0M
        71.2%
        7.8M
        61.7%
        1.2M
        200.0bp
        183.0bp
        0.6M
        0.5M
        0.5M
        0.0M
        0.0M
        0.1M
        0.8%
        0.1%
        3.4bp
        0.1%
        2.1bp
        2CLCmesc_016_RR_S17
        9.9M
        6.0M
        60.5%
        5.2M
        52.1%
        0.8M
        200.0bp
        183.5bp
        0.3M
        0.3M
        0.3M
        0.0M
        0.0M
        0.0M
        0.8%
        0.1%
        3.2bp
        0.1%
        2.2bp
        2CLCmesc_1_RR_S9
        3.5M
        2.1M
        61.0%
        1.8M
        52.9%
        0.3M
        200.0bp
        182.3bp
        0.1M
        0.1M
        0.1M
        0.0M
        0.0M
        0.0M
        1.3%
        0.1%
        5.0bp
        0.4%
        3.3bp
        2CLCmesc_1_S1
        13.9M
        2.9M
        20.7%
        2.5M
        18.3%
        0.3M
        200.0bp
        183.3bp
        0.8M
        0.7M
        0.8M
        0.0M
        0.0M
        0.0M
        0.6%
        0.1%
        3.2bp
        0.1%
        1.6bp
        2CLCmesc_2_RR_S10
        8.3M
        4.8M
        57.2%
        4.1M
        49.0%
        0.7M
        200.0bp
        181.5bp
        0.2M
        0.2M
        0.2M
        0.0M
        0.0M
        0.0M
        1.2%
        0.2%
        5.1bp
        0.4%
        3.5bp
        2CLCmesc_2_S2
        11.3M
        1.8M
        16.1%
        1.5M
        13.6%
        0.3M
        200.0bp
        180.7bp
        0.5M
        0.5M
        0.5M
        0.0M
        0.0M
        0.0M
        0.7%
        0.1%
        3.4bp
        0.0%
        1.5bp
        2CLCmesc_3_RR_S11
        13.2M
        9.1M
        68.6%
        7.9M
        59.5%
        1.2M
        200.0bp
        184.7bp
        1.1M
        1.0M
        1.0M
        0.0M
        0.0M
        0.1M
        1.1%
        0.1%
        4.2bp
        0.2%
        2.9bp
        2CLCmesc_3_S5
        20.6M
        12.5M
        60.9%
        10.9M
        53.3%
        1.6M
        200.0bp
        186.3bp
        3.7M
        3.5M
        3.5M
        0.0M
        0.0M
        0.1M
        0.7%
        0.1%
        2.4bp
        0.1%
        1.5bp
        2CLCmesc_4_RR_S12
        12.0M
        5.6M
        46.5%
        4.8M
        40.1%
        0.8M
        200.0bp
        185.2bp
        1.0M
        0.9M
        1.0M
        0.0M
        0.0M
        0.1M
        1.0%
        0.1%
        3.8bp
        0.2%
        2.5bp
        2CLCmesc_4_S6
        15.9M
        9.4M
        59.1%
        8.1M
        51.0%
        1.3M
        200.0bp
        185.1bp
        2.7M
        2.5M
        2.5M
        0.0M
        0.0M
        0.1M
        0.8%
        0.0%
        2.3bp
        0.1%
        1.5bp
        2CLCmesc_5_RR_S13
        6.7M
        4.9M
        72.6%
        4.2M
        62.7%
        0.7M
        200.0bp
        186.9bp
        1.1M
        1.1M
        1.1M
        0.0M
        0.0M
        0.0M
        0.9%
        0.1%
        3.5bp
        0.2%
        2.6bp
        2CLCmesc_5_S7
        16.9M
        12.9M
        76.4%
        11.2M
        66.2%
        1.7M
        200.0bp
        186.9bp
        4.0M
        3.8M
        3.9M
        0.0M
        0.0M
        0.1M
        0.7%
        0.0%
        2.2bp
        0.1%
        1.5bp
        2CLCmesc_6_RR_S14
        5.4M
        1.9M
        34.9%
        1.5M
        28.5%
        0.3M
        200.0bp
        183.9bp
        0.4M
        0.3M
        0.3M
        0.0M
        0.0M
        0.0M
        1.1%
        0.1%
        3.2bp
        0.1%
        2.5bp
        2CLCmesc_6_S8
        9.3M
        3.8M
        40.8%
        3.2M
        34.1%
        0.6M
        200.0bp
        185.3bp
        1.0M
        0.9M
        0.9M
        0.0M
        0.0M
        0.0M
        0.9%
        0.0%
        2.1bp
        0.1%
        1.6bp
        combined_003
        33.8M
        16.0M
        47.5%
        14.1M
        41.7%
        1.9M
        200.0bp
        183.5bp
        3.0M
        2.8M
        2.8M
        0.0M
        0.0M
        0.1M
        0.7%
        0.1%
        3.4bp
        0.1%
        1.9bp
        combined_004
        29.0M
        17.2M
        59.3%
        15.0M
        51.7%
        2.2M
        200.0bp
        185.8bp
        3.1M
        2.8M
        2.9M
        0.0M
        0.0M
        0.2M
        0.7%
        0.1%
        3.3bp
        0.1%
        2.0bp
        combined_1
        17.3M
        5.0M
        28.7%
        4.4M
        25.2%
        0.6M
        200.0bp
        182.9bp
        0.9M
        0.8M
        0.8M
        0.0M
        0.0M
        0.1M
        0.9%
        0.1%
        4.1bp
        0.2%
        2.8bp
        combined_2
        19.6M
        6.6M
        33.6%
        5.6M
        28.6%
        1.0M
        200.0bp
        181.3bp
        0.7M
        0.6M
        0.7M
        0.0M
        0.0M
        0.1M
        1.1%
        0.1%
        4.8bp
        0.3%
        3.4bp
        combined_3
        33.8M
        21.6M
        63.9%
        18.8M
        55.7%
        2.8M
        200.0bp
        185.6bp
        4.8M
        4.5M
        4.6M
        0.1M
        0.0M
        0.2M
        0.8%
        0.1%
        3.2bp
        0.1%
        2.4bp
        combined_4
        27.9M
        15.0M
        53.7%
        12.9M
        46.3%
        2.1M
        200.0bp
        185.1bp
        3.7M
        3.4M
        3.5M
        0.0M
        0.0M
        0.1M
        0.8%
        0.1%
        2.9bp
        0.1%
        2.1bp
        combined_5
        23.6M
        17.8M
        75.3%
        15.4M
        65.2%
        2.4M
        200.0bp
        186.9bp
        5.2M
        4.9M
        5.0M
        0.1M
        0.0M
        0.2M
        0.8%
        0.1%
        2.6bp
        0.1%
        2.0bp
        combined_6
        14.7M
        5.7M
        38.6%
        4.7M
        32.1%
        1.0M
        200.0bp
        184.8bp
        1.3M
        1.3M
        1.3M
        0.0M
        0.0M
        0.0M
        0.9%
        0.0%
        2.5bp
        0.1%
        2.0bp

        Alignment Scores

        Created with MultiQC

        FastQC

        Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 0/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
        44
        5940931
        0.5637%
        AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
        38
        2743254
        0.2603%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        35
        1011753
        0.0960%
        AGGCCCGGTGGGGAAGGTGGCTCGGGGGGGGCGGCGCGTCTCAGGGCGCG
        20
        842347
        0.0799%
        GGAAGGCCCGGTGGGGAAGGTGGCTCGGGGGGGGCGGCGCGTCTCAGGGC
        12
        276892
        0.0263%
        GGTTACCCAAAAAATGAATTTAAGTTCAATTTTAAACTTGCTAAAAAAAC
        12
        138855
        0.0132%
        GGCGAGCTCAGGGAGGACAGAAACCTCCCGTGGAGCAGAAGGGCAAAAGC
        12
        377885
        0.0359%
        GGTGGCGCACGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGACAGGAGGA
        10
        124094
        0.0118%
        GGTGAACTATGCCTGGGCAGGGCGAAGCCAGAGGAAACTCTGGTGGAGGT
        10
        226452
        0.0215%
        GCGAGCTCAGGGAGGACAGAAACCTCCCGTGGAGCAGAAGGGCAAAAGCT
        10
        229390
        0.0218%
        AGGTGGCTCGGGGGGGGCGGCGCGTCTCAGGGCGCGCCGAACCACCTCAC
        9
        130412
        0.0124%
        CCTCACCCGGCCCGGACACGGACAGGATTGACAGATTGATAGCTCTTTCT
        8
        384780
        0.0365%
        AGAAAAGTTACCACAGGGATAACTGGCTTGTGGCGGCCAAGCGTTCATAG
        8
        312887
        0.0297%
        TGGTGAACTATGCCTGGGCAGGGCGAAGCCAGAGGAAACTCTGGTGGAGG
        8
        98240
        0.0093%
        GGGCGAAGCCAGAGGAAACTCTGGTGGAGGTCCGTAGCGGTCCTGACGTG
        8
        113197
        0.0107%
        CCGGGCGTCGTCGCGCCGTCGGGTCCCGGGGGGACCGTCGGTCACGCGTC
        8
        161159
        0.0153%
        CGGTGGCGCACGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGACAGGAGG
        8
        147475
        0.0140%
        AGTGACGAAAAATAACAATACAGGACTCTTTCGAGGCCCTGTAATTGGAA
        8
        148611
        0.0141%
        GCAGAATTCACCAAGCGTTGGATTGTTCACCCACTAATAGGGAACGTGAG
        6
        170828
        0.0162%
        GCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGCGTTGGATTGTTCAC
        6
        118576
        0.0113%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        FastQCfastqc0.12.1
        GUNZIP_FASTAgunzip1.1
        MTX_TO_H5ADanndata0.10.8
        pandas2.2.2
        python3.12.5
        scanpy1.10.2
        STAR_ALIGNstar2.7.10b
        WorkflowNextflow24.10.0
        nf-core/scrnaseqv3.1.0dev

        nf-core/scrnaseq Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/scrnaseq

        Methods

        Data was processed using nf-core/scrnaseq v3.1.0dev (doi: 10.5281/zenodo.3568187) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.10.0 (Di Tommaso et al., 2017) with the following command:

        nextflow run ../pipeline -profile daisybio,keep_work,apptainer,mouse,star_plate -resume

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/scrnaseq Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/scrnaseq

        Input/output options

        input
        samplesheet.csv
        outdir
        star_plate

        Mandatory arguments

        aligner
        star
        barcode_whitelist
        ../../data/reference/plate.txt
        protocol
        CB_UMI_Simple

        Skip Tools

        skip_cellbender
        true

        Reference genome options

        fasta
        ../../data/reference/mouse/GRCm39.genome.fa.gz
        gtf
        ../../data/reference/mouse/gencode.vM36.annotation.gtf
        igenomes_base
        /nfs/data/references/igenomes
        save_align_intermeds
        true
        save_reference
        true

        STARSolo Options

        star_feature
        Gene Velocyto
        star_index
        ../../data/reference/mouse/star

        Institutional config options

        config_profile_contact
        Johannes Kersting (@JohannesKersting)
        config_profile_description
        DaiSyBio cluster profile provided by nf-core/configs.
        config_profile_url
        https://www.mls.ls.tum.de/daisybio/startseite/

        Generic options

        trace_report_suffix
        2025-01-21_17-29-03

        Core Nextflow options

        configFiles
        N/A
        containerEngine
        apptainer
        launchDir
        /nfs/data/COST_IBD/VASA-Seq/scrnaseq/run
        profile
        daisybio,keep_work,apptainer,mouse,star_plate
        projectDir
        /nfs/data/COST_IBD/VASA-Seq/scrnaseq/pipeline
        runName
        backstabbing_mercator
        userName
        n.trummer
        workDir
        /nfs/scratch/nf-core_work/nfs.data.COST_IBD.VASA-Seq.scrnaseq.run